Hematopoietic stem cell transplantation (HSCT) has been employed clinically for the therapy of a wide variety of acquired neoplastic and nonmalignant disorders. However, these immunocompromised patients remain at high risk of developing many serious and often life threatening complications. Occurring in up to 70% of allogeneic HSCT patients, respiratory complications are a leading cause of morbidity and mortality in this population. A rapid identification of the cause and institution of specific therapy is critical to achieve a good outcome. Unfortunately, early recognition and definitive diagnosis of such complications are difficult. In the presence of a modest immune response and neutropenia, the changes on a chest radiograph corresponding to early infectious and non-infectious processes are subtle, nonspecific and may not be recognized. Due to its greater sensitivity, thoracic computed tomography (CT) scan has been proposed to replace the plain chest radiograph (CXR) in the primary evaluation of immunocompromised patients. In the last five years in our institution, thoracic low dose CT (LDCT) scan has become the standard of care and has replaced the CXR in evaluating fever or respiratory symptoms in this group of patients. The published data concerning the use of LDCT scan of the chest as the primary tool for evaluation of this group of patients is limited. Our aim is to summarize the current knowledge in this matter and to add some new perspective from our experience.